[Repo Assist] feat: enforce ServerConfig.Tools as an allow-list at registration time

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Summary

The tools field in server configuration was parsed and stored but never applied — all backend tools were always exposed regardless of configuration. This has been documented as a known limitation in docs/CONFIGURATION.md.

This PR implements the allow-list enforcement so the tools field works as documented.

Root cause

registerToolsFromBackend fetched tools from the backend and registered all of them without consulting serverCfg.Tools.

Fix

After unmarshalling the tools/list response, check whether the server config has a non-empty Tools allow-list. If so, filter the tool slice in-place before the registration loop, keeping only the listed tools.

if serverCfg, ok := us.cfg.Servers[serverID]; ok && serverCfg != nil && len(serverCfg.Tools) > 0 {
    allowedTools := make(map[string]struct{}, len(serverCfg.Tools))
    for _, name := range serverCfg.Tools {
        allowedTools[name] = struct{}{}
    }
    originalCount := len(listResult.Tools)
    filtered := listResult.Tools[:0]
    for _, tool := range listResult.Tools {
        if _, allowed := allowedTools[tool.Name]; allowed {
            filtered = append(filtered, tool)
        }
    }
    listResult.Tools = filtered
    // log skipped count...
}

When Tools is empty/nil (the default), all backend tools are exposed — existing behaviour is preserved.

Changes

• internal/server/unified.go — allow-list filtering added to registerToolsFromBackend
• internal/server/register_tools_from_backend_test.go — two new tests: ToolsAllowList (non-empty allow-list filters correctly) and EmptyToolsAllowList (empty list exposes all tools)
• docs/CONFIGURATION.md — updated tools field description to reflect enforcement

Trade-offs

• The filter is applied at registration time (startup), so changes to the config require a gateway restart.
• Tools not in the allow-list are silently skipped; a log message records how many were filtered.

Test Status

Build and tests require Go 1.25.0, which is unavailable in the sandbox environment (Go 1.24.13 is present but the go.mod requires ≥ 1.25.0 and the Go toolchain download is blocked by the network firewall). This is an infrastructure limitation — the CI pipeline (which has Go 1.25) should run the tests normally.

The logic change is minimal and localised to a single conditional block inserted before the existing registration loop.

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